Just take 10 minutes and skim the book chapters. The rules of the script are nowhere near as loose as you say. For example, Linear B doesn’t differentiate between k/g/kh like alphabetic Greek does (κ,γ,χ) — an important distinction, sure, but its loss doesn’t let you turn anything into anything else.

So with the Theban tablets, if the decipherment were false it should have yielded nonsense when applied to unknown texts.